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- EMDB-30536: Photosystem I-LHCI-LHCII of Chlamydomonas reinhardtii -

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Basic information

Entry
Database: EMDB / ID: EMD-30536
TitlePhotosystem I-LHCI-LHCII of Chlamydomonas reinhardtii
Map data
Sample
  • Complex: Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtii
    • Complex: Photosystem I
      • Protein or peptide: x 12 types
    • Complex: LHCI
      • Protein or peptide: x 1 types
    • Complex: LHCII
      • Protein or peptide: x 11 types
  • Ligand: x 12 types
Function / homology
Function and homology information


plastoglobule / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / : / photosystem I / chloroplast envelope / photosystem I / photosystem II ...plastoglobule / photosynthesis, light harvesting / chloroplast thylakoid lumen / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / : / photosystem I / chloroplast envelope / photosystem I / photosystem II / photosynthetic electron transport in photosystem I / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / metal ion binding
Similarity search - Function
: / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK ...: / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic ...Photosystem I reaction center subunit VIII / Chlorophyll a-b binding protein, chloroplastic / PSI subunit V / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1 / Photosystem I reaction center subunit IV, chloroplastic / Photosystem I reaction center subunit III, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit psaK, chloroplastic / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant) / Chlamydomonas smithii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsWang WD / Shen LL / Huang ZH / Han GY / Zhang X / Shen JR
Funding support China, 3 items
OrganizationGrant numberCountry
Chinese Academy of SciencesQYZDY-SSW-SMC003 China
National Basic Research Program of China (973 Program)2015CB150100 China
Chinese Academy of SciencesXDB17000000 China
CitationJournal: Science / Year: 2018
Title: Structure of the maize photosystem I supercomplex with light-harvesting complexes I and II.
Authors: Xiaowei Pan / Jun Ma / Xiaodong Su / Peng Cao / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li /
Abstract: Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light- ...Plants regulate photosynthetic light harvesting to maintain balanced energy flux into photosystems I and II (PSI and PSII). Under light conditions favoring PSII excitation, the PSII antenna, light-harvesting complex II (LHCII), is phosphorylated and forms a supercomplex with PSI core and the PSI antenna, light-harvesting complex I (LHCI). Both LHCI and LHCII then transfer excitation energy to the PSI core. We report the structure of maize PSI-LHCI-LHCII solved by cryo-electron microscopy, revealing the recognition site between LHCII and PSI. The PSI subunits PsaN and PsaO are observed at the PSI-LHCI interface and the PSI-LHCII interface, respectively. Each subunit relays excitation to PSI core through a pair of chlorophyll molecules, thus revealing previously unseen paths for energy transfer between the antennas and the PSI core.
History
DepositionSep 10, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d0j
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30536.png

Downloads & links

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Map

FileDownload / File: emd_30536.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 0.5
Minimum - Maximum-1.7253877 - 5.004408
Average (Standard dev.)-0.0015372316 (±0.08526802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 470.52002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z470.520470.520470.520
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.7255.004-0.002

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Supplemental data

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Sample components

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Entire : Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtii

EntireName: Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtii
Components
  • Complex: Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtii
    • Complex: Photosystem I
      • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
      • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
      • Protein or peptide: Photosystem I iron-sulfur center
      • Protein or peptide: Photosystem I reaction center subunit II, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit IV, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit V, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit VI, chloroplastic
      • Protein or peptide: Photosystem I reaction center subunit VIII
      • Protein or peptide: Photosystem I reaction center subunit IX
      • Protein or peptide: Photosystem I reaction center subunit psaK, chloroplastic
      • Protein or peptide: Photosystem I subunit O
    • Complex: LHCI
      • Protein or peptide: PSI subunit V
    • Complex: LHCII
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
      • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL B
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Supramolecule #1: Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtii

SupramoleculeName: Photosystem I-LHCI-LHCII supercomplex of Chlamydomonas reinhardtii
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Supramolecule #2: Photosystem I

SupramoleculeName: Photosystem I / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#11, #13
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Supramolecule #3: LHCI

SupramoleculeName: LHCI / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #12
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Supramolecule #4: LHCII

SupramoleculeName: LHCII / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #14-#24

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 81.992758 KDa
SequenceString: KVKIAVDRNP VETSFEKWAK PGHFSRTLSK GPNTTTWIWN LHADAHDFDS HTSDLEEISR KVFSAHFGQL GIIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQEILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLVMA A AMFFAGWF ...String:
KVKIAVDRNP VETSFEKWAK PGHFSRTLSK GPNTTTWIWN LHADAHDFDS HTSDLEEISR KVFSAHFGQL GIIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQEILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLVMA A AMFFAGWF HYHKAAPKLE WFQNVESMLN HHLGGLLGLG SLAWAGHQIH VSLPVNKLLD AGVDPKEIPL PHDLLLNRAI MA DLYPSFA KGIAPFFTLN WSEYSDFLTF KGGLNPVTGG LWLSDTAHHH VAIAVLFLVA GHMYRTNWGI GHSMKEILEA HRG PFTGEG HVGLYEILTT SWHAQLAINL ALFGSLSIIV AHHMYAMPPY PYLATDYGTQ LSLFTHHTWI GGFCIVGAGA HAAI FMVRD YDPTNNYNNL LDRVIRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPVFAQW IQNTH FLAP QLTAPNALAA TSLTWGGDLV AVGGKVAMMP ISLGTSDFMV HHIHAFTIHV TVLILLKGVL FARSSRLIPD KANLGF RFP CDGPGRGGTC QVSAWDHVFL GLFWMYNSLS IVIFHFSWKM QSDVWGTVTA SGVSHITGGN FAQSANTING WLRDFLW AQ SSQVIQSYGS ALSAYGLIFL GAHFVWAFSL MFLFSGRGYW QELIESIVWA HNKLKVAPAI QPRALSITQG RAVGVAHY L LGGIATTWSF FLARIISVG

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 82.05307 KDa
SequenceString: ATKLFPKFSQ GLAQDPTTRR IWYGLAMAHD FESHDGMTEE NLYQKIFASH FGQLSIIFLW TSGNLFHVAW QGNFEQWVTD PVHIRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNISTSG VYQWWYTIGM RTNQDLYVGS VFLALVSAIF LFAGWLHLQP N FQPSLSWF ...String:
ATKLFPKFSQ GLAQDPTTRR IWYGLAMAHD FESHDGMTEE NLYQKIFASH FGQLSIIFLW TSGNLFHVAW QGNFEQWVTD PVHIRPIAH AIWDPHFGQP AVEAFTRGGA SGPVNISTSG VYQWWYTIGM RTNQDLYVGS VFLALVSAIF LFAGWLHLQP N FQPSLSWF KDAESRLNHH LSGLFGVSSL AWTGHLVHVA IPESRGQHVG WDNFLSVLPH PQGLTPFFTG NWAAYAQSPD TA SHVFGTA QGSGQAILTF LGGFHPQTQS LWLTDMAHHH LAIAVIFIVA GHMYRTNFGI GHRMQAILEA HTPPSGSLGA GHK GLFDTV NNSLHFQLGL ALASVGTITS LVAQHMYSLP PYAFQAIDFT TQAALYTHHQ YIAGFIMCGA FAHGAIFFIR DYDP EQNKG NVLARMLDHK EALISHLSWV SLFLGFHTLG LYVHNDVMQA FGTPEKQILI EPVFAQWIQA AHGKALYGFD FLLSS KTSA AFANGQSLWL PGWLDAINNN QNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAY DAFYLAVFWM LNTIGWVTFY WHWKHLTLWQ GNVAQFDESS TYLMGWLRDY LWLNSSQLIN GYNPFGM NS LSVWAWTFLF GHLIYATGFM FLISWRGYWQ ELIETLVWAH EKTPLANLVY WKDKPVALSI VQARLVGLAH FSVGYIFT Y AAFLIASTSG RFG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 8.73813 KDa
SequenceString:
AHIVKIYDTC IGCTQCVRAC PLDVLEMVPW DGCKASQMAS APRTEDCVGC KRCETACPTD FLSVRVYLGS ESTRSMGLSY

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Macromolecule #4: Photosystem I reaction center subunit II, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit II, chloroplastic
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 16.123686 KDa
SequenceString:
WTVPTLNPDT PSPIFGGSTG GLLRKAQTEE FYVITWEAKK EQIFEMPTGG AAIMRQGPNL LKFGKKEQCL ALTTQLRNKF KLTPCFYRV FPDGKVQYLH PADGVYPEKV NAGRVGANQN MRRIGQNVNP IKVKFSGRMM SPAEI

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Macromolecule #5: Photosystem I reaction center subunit IV, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit IV, chloroplastic
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 7.021877 KDa
SequenceString:
EVGPKRGSLV KILRPESYWF NQVGKVVSVD QSGVRYPVVV RFENQNYAGV TTNNYALDEV VAA

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Macromolecule #6: Photosystem I reaction center subunit F, Photosystem I reaction c...

MacromoleculeName: Photosystem I reaction center subunit F, Photosystem I reaction center subunit III, chloroplastic
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 17.957773 KDa
SequenceString:
DIAGLTPCSE SKAYAKLEKK ELKTLEKRLK QYEADSAPAV ALKATMERTK ARFANYAKAG LLCGNDGLPH LIADPGLALK YGHAGEVFI PTFGFLYVAG YIGYVGRQYL IAVKGEAKPT DKEIIIDVPL ATKLAWQGAG WPLAAVQELQ RGTLLEKEEN I TVSPR

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Macromolecule #7: Photosystem I reaction center subunit V, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit V, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 9.572677 KDa
SequenceString:
LDPQIVISGS TAAFLAIGRF VFLGYQRREA NFDSTVGPKT TGATYFDDLQ KNSTIFATND PAGFNIIDVA GWGALGHAVG FAVLAINSL QG

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Macromolecule #8: Photosystem I reaction center subunit VI, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit VI, chloroplastic
type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 11.053327 KDa
SequenceString:
KYGENSRYFD LQDMENTTGS WDMYGVDEKK RYPDNQAKFF TQATDIISRR ESLRALVALS GIAAIVTYGL KGAKDADLPI TKGPQTTGE NGKGGSVRSR L

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Macromolecule #9: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 3.970731 KDa
SequenceString:
PFVPPSWAPS VFVPLTGLVL PAIAMATLFV YIEKEAP

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Macromolecule #10: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 4.750509 KDa
SequenceString:
MKDFTTYLST APVIATIWFT FTAGLLIEIN RYFPDPLVFS F

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Macromolecule #11: Photosystem I reaction center subunit psaK, chloroplastic

MacromoleculeName: Photosystem I reaction center subunit psaK, chloroplastic
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 8.259625 KDa
SequenceString:
FIGSSTNLIM VASTTATLAA ARFGLAPTVK KNTTAGLKLV DSKNSAGVIS NDPAGFTIVD VLAMGAAGHG LGVGIVLGLK GIGAL

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Macromolecule #12: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 16.449949 KDa
SequenceString:
KKAQVISPVN GDPFVGMLET PVTSAPIVAT YLSNLPAYRT GVAPVLRGVE IGLAHGFLLA GPFIKLGPLR NVPETAEIAG SLSAAGLVL ILALCLSIYG SAQFQSTPSI GVKTLSGRSV ARDPLFSADG WSEFAAGFLV GGEAGVAWAY VCTQILPYYS

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Macromolecule #13: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 10.129586 KDa
SequenceString:
ASNKSFPRDW VKTDPLVPVL GFAGWTIPAN IGVSAFGGQS LFGLFTQSIG ENLAHFPTGP ALDDKFWLYL ITYHLGLFLT ITLGQIGVQ GRKQ

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Macromolecule #14: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 14 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 23.69068 KDa
SequenceString: IEFYGPNRAK WLGPYSENAT PAYLTGEFPG DYGWDTAGLS ADPETFKRYR ELELIHARWA MLGALGCITP ELLAKSGTQF GEAVWFKAG AQIFSEGGLD YLGNPSLVHA QNIVATLAVQ VILMGLVEGY RVNGGPAGEG LDPLYPGESF DPLGLADDPD T FAELKVKE ...String:
IEFYGPNRAK WLGPYSENAT PAYLTGEFPG DYGWDTAGLS ADPETFKRYR ELELIHARWA MLGALGCITP ELLAKSGTQF GEAVWFKAG AQIFSEGGLD YLGNPSLVHA QNIVATLAVQ VILMGLVEGY RVNGGPAGEG LDPLYPGESF DPLGLADDPD T FAELKVKE IKNGRLAMFS MFGFFVQAIV TGKGPIQNLD DHLSNPTVNN AFAFATKFTP S

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Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 25.157326 KDa
SequenceString: KK(TPO)AAKAAAP KSSGVEFYGP NRAKWLGPYS ENSTPAYLTG EFPGDYGWDT AGLSADPETF KRYRELELIH ARWAML GAL GCLTPELLAK NGTKFGEAVW FKAGAQIFSE GGLDYLGNPS LVHAQNIVAT LAVQVILMGL IEGYRVNGGP AGEGLDP LY PGESFDPLGL ...String:
KK(TPO)AAKAAAP KSSGVEFYGP NRAKWLGPYS ENSTPAYLTG EFPGDYGWDT AGLSADPETF KRYRELELIH ARWAML GAL GCLTPELLAK NGTKFGEAVW FKAGAQIFSE GGLDYLGNPS LVHAQNIVAT LAVQVILMGL IEGYRVNGGP AGEGLDP LY PGESFDPLGL ADDPDTFAEL KVKEIKNGRL AMFSMFGFFV QAIVTGKGPV QNLDDHLANP TVNNAFAFAT KFTPSA

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Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 20.368023 KDa
SequenceString: KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP ...String:
KAGNWLPGSD APAWLPDDLP GNYGFDPLSL GKEPASLKRF TESEVIHGRW AMLGVAGSLA VELLGYGNWY DAPLWAVNGG KATWFGIEV PFDLNALLAF EFVAMAAAEG QRGDAGGVVY PGGAFDPLGF AKDSSKSGEL KLKEIKNGRL AMVAFLGFVA Q HAATGKGP IAALGEHLAN PWGANFATNG ISVPFF

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Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 21.986465 KDa
SequenceString: RPMWYPGATA PAHLDGSMLG DYGFDPLRLG VNKDNLKWFR EAELTNGRWA MAAVVGILFT DAVGLPKFWT AGAEKYALDN QTLALIEVA VFAVLEGKRY EIYKKTGETG FLSFAPFDPM GMKSEEMKLK ELKNGRLAML AFLGFCSQAA VYGKGPIETL Q LHLADPGH ...String:
RPMWYPGATA PAHLDGSMLG DYGFDPLRLG VNKDNLKWFR EAELTNGRWA MAAVVGILFT DAVGLPKFWT AGAEKYALDN QTLALIEVA VFAVLEGKRY EIYKKTGETG FLSFAPFDPM GMKSEEMKLK ELKNGRLAML AFLGFCSQAA VYGKGPIETL Q LHLADPGH NNIYTSSVGP ETAVTVAVLC VLPMIIEATK TLN

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Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 22.090312 KDa
SequenceString: LPGDFGFDPL GLLDPVNSGG FIEPKWLQYS EVIHARWAML GAAGCIAPEV LGAAGLIPDA TNIKWFESGV IPPAGSYNGY WADPYTIFF VEIVAMQFAE LRRLQDFRYP GSMGQQYFLG LEAIFKGSGD AAYPGGPFFN LFNLGKTEAA MKELKLKEIK N GRLAMLAM ...String:
LPGDFGFDPL GLLDPVNSGG FIEPKWLQYS EVIHARWAML GAAGCIAPEV LGAAGLIPDA TNIKWFESGV IPPAGSYNGY WADPYTIFF VEIVAMQFAE LRRLQDFRYP GSMGQQYFLG LEAIFKGSGD AAYPGGPFFN LFNLGKTEAA MKELKLKEIK N GRLAMLAM LGYGAQAVMT GKGPFQNLVE HLADPVNNNI LTNFA

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Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 22.49059 KDa
SequenceString: LPSWMPGADL PGYLNGTLPG DFGFDPLYLG QDPVKLKWYA QAELMNARFA MLAVAGILVP ELLSNIGFSW PGAGVAWYDA GKFEYFAPA SSLFGVQMLL FAWVEIRRYQ DFVKPGSANQ DPIFTNNKLP DGNEPGYPGG IFDPFGWSKG DIKSLKLKEI K NGRLAMLA ...String:
LPSWMPGADL PGYLNGTLPG DFGFDPLYLG QDPVKLKWYA QAELMNARFA MLAVAGILVP ELLSNIGFSW PGAGVAWYDA GKFEYFAPA SSLFGVQMLL FAWVEIRRYQ DFVKPGSANQ DPIFTNNKLP DGNEPGYPGG IFDPFGWSKG DIKSLKLKEI K NGRLAMLA FAGFIGQAYT TGTTPLKNLS THLADPWSTT VWQNDLA

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Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 24.879588 KDa
SequenceString: RKLWAPGVVA PEYLKGDLAG DYGWDPLGLG ADPTALKWYR QSELQHARWA MLGVAGVLVQ EIVKPDVYFY EAGLPQNLPE PFTNINMGG LLAWEFILMH WVEVRRWQDY KNFGSVNEDP IFKGNKVPNP EMGYPGGIFD PFGFSKGNLK ELQTKEIKNG R LAMIAYMA ...String:
RKLWAPGVVA PEYLKGDLAG DYGWDPLGLG ADPTALKWYR QSELQHARWA MLGVAGVLVQ EIVKPDVYFY EAGLPQNLPE PFTNINMGG LLAWEFILMH WVEVRRWQDY KNFGSVNEDP IFKGNKVPNP EMGYPGGIFD PFGFSKGNLK ELQTKEIKNG R LAMIAYMA FILQAQATGK GPLAALSAHL SNPFGNNILK NIGTCTVPHS VDVQGLTIPL TCLWPGS

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Macromolecule #21: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 25.025 KDa
SequenceString: SRPLWLPGST PPAHLKGDLP GDFGFDPLGL GANAESLKWF KESELVHSRW AMAAVAGILV QEIVRPDVFW YNAGKEVESP LGPLGLLAV EFFLMHWVEV RRWQDLRKPG SVDQDPIFSQ YKLPPHEVGY PGGVFAPFIP GDLAELKVKE IKNGRLAMLA F VGFVMAAQ ...String:
SRPLWLPGST PPAHLKGDLP GDFGFDPLGL GANAESLKWF KESELVHSRW AMAAVAGILV QEIVRPDVFW YNAGKEVESP LGPLGLLAV EFFLMHWVEV RRWQDLRKPG SVDQDPIFSQ YKLPPHEVGY PGGVFAPFIP GDLAELKVKE IKNGRLAMLA F VGFVMAAQ VTGKGPIAAL QEHLADPWGT TIFSKAAVVP GQAVAPPCKI PASVSYKGIE IPTPCFLQGL WP

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Macromolecule #22: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 23.30534 KDa
SequenceString: VRPVWFPGNP PPAHLDGSLA GDYGFDPLFL GQEPQTLKWY VQAELVHGRF AMLGAAGIIL TSIGAKVGLG FPEWYDAGKV VVEKNNIDF PTLMVIQFYL MGWAETKRWY DFKNPGSQAD GSFLGFTEEF KGLENGYPGG RFFDPMGLSR GDAAKYQEYK Q KEVKNGRL ...String:
VRPVWFPGNP PPAHLDGSLA GDYGFDPLFL GQEPQTLKWY VQAELVHGRF AMLGAAGIIL TSIGAKVGLG FPEWYDAGKV VVEKNNIDF PTLMVIQFYL MGWAETKRWY DFKNPGSQAD GSFLGFTEEF KGLENGYPGG RFFDPMGLSR GDAAKYQEYK Q KEVKNGRL AMIACLGFAA QYAATGKGPL DNLADHLADP NHVNFATNGV SNPIA

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Macromolecule #23: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 23.293613 KDa
SequenceString: RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK ...String:
RQSWLPGSQI PAHLDTPAAQ ALAGNFGFDP LGLGKDPVAL RWYQQAELIH CRTAMAGVAG ILIPGLLTKA GALNVPEWYD AGKVAIENS FAPWGSLLAV QLFLCGFVEA KRWQDIRKPG SQGEPGSFLG FEASLKGTSE LGYPGGPFDP LGLSKEADKW A DWKLKEVK NGRLAMLAFL GFVAQKYATG AGPVDNLAAH LKDPWHVNYA TNGVSLPFL

+
Macromolecule #24: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas smithii (plant)
Molecular weightTheoretical: 19.772625 KDa
SequenceString:
PTWLPGLNPP AHLKGALAGD NGFDPLGLGQ DEGRLKWYAE AEKTNGRWAM MAVAGILGQE LLGVTPAWWE AGAKEYDIPA QALTPIEFI VMGFLEIKRY QGFKQTGTSG FINSFPFDPA GMNSPSMATK EVKNGRLAMV AFIGFCVQAL ATRTQPIEGL T AHLADPFG KNITYYLTHL PETL

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Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 276 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #26: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 26 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #27: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 27 / Number of copies: 20 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

+
Macromolecule #28: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 28 / Number of copies: 37 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #29: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 29 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #30: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 30 / Number of copies: 2 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #31: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 31 / Number of copies: 1 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #32: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 32 / Number of copies: 10 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #33: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 33 / Number of copies: 56 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #34: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 34 / Number of copies: 34 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Lutein

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Macromolecule #35: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 35 / Number of copies: 6 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / Violaxanthin

+
Macromolecule #36: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 36 / Number of copies: 6 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 283763

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